Background: Alopecia areata (AA) is higher in patients with thyroid dysfunctions such as Hashimoto's thyroiditis and Graves' disease than in general population. Our aim was to assess AA frequency in patients with thyroid diseases. Materials and Methods: This prospective study included 550 patients with autoimmune thyroid disease (AITD), 126 patients with non-AITD (NAITD), and 100 healthy subjects. Results: Twenty-eight (4.1%) patients were diagnosed with AA based on either medical history or physical examination (P = 0.039). AA was not determined in healthy subjects. The rate of AA was higher among the patients with NAITD than those with AITD (5.6% vs. 3.8%; P = 0.075). Among the AITD patients, 5 (23.8%) patients were diagnosed with AA after being diagnosed with thyroid disease, whereas 15 (71.4%) patients were diagnosed with AA before being diagnosed with thyroid disease. The mean ages at the diagnosis of AITD and at the onset of AA were 36.6 ± 10.8 years and 30.3 ± 13.0 years, respectively. Among the NAITD patients, the mean ages at the onset of thyroid disease and at the onset of AA were 45.3 ± 9.3 years and 37.3 ± 13.3 years, respectively. Other autoimmune-based diseases such as vitiligo, chronic urticaria, and type 1 diabetes were also detected. The patchy pattern of AA was the most common type (n = 27). Conclusions: The frequency of AA was higher in patients with NAITD and AITD compared to the healthy population. Clinicians should be aware of these findings, and accordingly, it would be suitable for them to screen AA patients for thyroid diseases.